Ephedra torreyana is known to form hybrids with two other species of Ephedra as reported and described by H. C. Cutler (1939). The first of these is E . × intermixta Cutler, the hybrid between E . torreyana and E . trifurca . This hybrid occurs in a small area of southwestern New Mexico (near Engle, Sierra County) within the zone of sympatry of the two parental species; it may be fertile (mature seeds are formed). It is intermediate in most characters but can be identified by its combination of the spinelike terminal buds of E . trifurca and the scabrous, light yellow seeds of E . torreyana .

The second hybrid is Ephedra × arenicola Cutler, the hybrid between E . torreyana and E . cutleri . This hybrid is known only from the type locality in extreme northeastern Arizona (near Dennehotso, Apache County) in an area of sympatry of the parental species. This hybrid is intermediate in most characters, but it can be distinguished by its combination of the setaceous leaves, viscid stems, and long-pedunculate seed cones of E . cutleri with the persistent, whorled leaves of E . torreyana .